SMTL ID : 8pje.2 (1 other biounit)

Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus haemagglutinin (HA)306-318 PKYVKQNTLKLAT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 7 residues within 4Å: Chain A: P.100, V.101, E.102, W.182, F.184, D.185 Chain B: Y.106 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.101, A:D.185 Water bridges: A:E.102, A:E.102 Salt bridges: A:E.102, A:E.102

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: F.157, L.158, P.159, S.160, D.163, Y.165, W.182 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.158, A:S.160, A:D.163 Water bridges: A:S.160, A:F.184 EDO.3: 5 residues within 4Å: Chain A: Q.22, S.23, G.24, M.40, I.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.24, A:G.24 EDO.4: 3 residues within 4Å: Chain A: F.55 Chain B: S.92, F.93 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain A: G.53, R.54, F.55, A.56, S.57 Chain C: P.1 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:P.1, C:P.1, A:G.53 EDO.6: 3 residues within 4Å: Chain A: I.86, T.87, N.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.88 Water bridges: A:N.88, A:N.88 EDO.7: 3 residues within 4Å: Chain A: V.89, P.90, K.115 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain B: E.180, H.181, V.184, T.185, S.186, P.187 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.181 EDO.9: 2 residues within 4Å: Chain B: W.192, R.193 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.192, B:R.193, B:R.193 EDO.10: 3 residues within 4Å: Chain B: P.101, K.102, V.103 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.103 Water bridges: B:E.100 EDO.11: 3 residues within 4Å: Chain B: S.46, D.47, V.48 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain B: A.53, E.56, R.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.59 Water bridges: B:E.56 EDO.16: 4 residues within 4Å: Chain A: F.58 Chain C: Y.3, V.4, K.5 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.3, C:K.5, C:K.5 Water bridges: A:E.59 EDO.17: 4 residues within 4Å: Chain B: Y.64 Chain C: L.11, A.12, T.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.13, C:T.13 EDO.18: 4 residues within 4Å: Chain B: Y.64, Q.68 Chain C: L.9, K.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.10

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 5 residues within 4Å: Chain A: R.48, N.98, V.108, Y.154 Chain B: D.156 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.156, A:R.48, A:R.48 Water bridges: A:S.137 GOL.14: 6 residues within 4Å: Chain B: I.131, E.132, V.133, S.148, T.161, V.163 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.131, B:V.133, B:S.148 Water bridges: B:I.131 GOL.15: 5 residues within 4Å: Chain B: E.26, R.27, V.28, V.79, R.84 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.26, B:R.27, B:V.28, B:V.28, B:R.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hulin-Curtis, S. et al., A targeted single mutation in influenza A virus universal epitope transforms immunogenicity and protective immunity via CD4 + T cell activation. Cell Rep (2024)

Release Date

2024-06-19

Peptides

HLA class II histocompatibility antigen, DR alpha chain: A
HLA class II histocompatibility antigen, DRB1 beta chain: B
Hemagglutinin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

HLA class II histocompatibility antigen, DR alpha chain

HLA class II histocompatibility antigen, DRB1 beta chain

Hemagglutinin

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